charged ligand for autodock

Dear Autodock users,
 What is the best way to assign charges to an ionized ligand for docking
 with Autodock?  I have been using AutoDockTools to add Gasteiger charges
 to my ligands, and then editing the pdbq file to remove a hydrogen and
 add a -1 charge to the nitrogen that is ionized.  But I'm sure that
 isn't an accurate way to do it.  If I remove the hydrogen before feeding
 the coordinates to ADT, the charges are different, but the overall
 charge is 0.0 (neutral), which isn't what I want.  Is there any way to
 tell ADT that a ligand should be charged?  If not, how should I
 calculate, or approximate, the partial charges on my ionized ligand?
 P.S.  The group on the ligand that is ionized is    -S-NH2
         Susan Heffron
 Dept. of Physiology and Biophysics
 University of California, Irvine
  Irvine, CA  92697-4560   U.S.A.
     phone:  (949) 824-4625
     FAX:    (949) 824-8540